Project Summary The specific aim of this proposal is to carry out an annual, full-week course in advanced gene mapping at The Rockefeller University in New York. The course is directed towards advanced researchers who are familiar with the basic aspects of statistical genetics but who need to become more proficient in the analysis of complex traits. The course will be held in the Great Hall in Welch which is equipped for the course with laptops running Linux. Thirty students will be accepted for each course.. Travel stipends will be provided to five of the participants who are either pre-doctoral students or post-doctoral fellows to cover the cost of airfare, hotel and board. The course consists of two components: lectures on important, current topics in gene mapping, as well as hands on exercises to be carried out with the latest freeware software programs. The current emphasis of the course is association analysis of rare variants obtained from next generation sequence data. For the next Advanced Gene Mapping course held January 25-29, 2016 the topics will include: analysis of whole genome association studies; analysis of rare variants using next generation sequence data; analysis of qualitative and quantitative traits (population and family-based data); mixed linear models; eQTL mapping; prediction models using RNAseq and array data; inferences for heritability estimation and prediction; functional predication of variant sites, variant annotation; variant calling, controlling for population substructure/admixture (principal components analysis/multidimensionality scaling); data quality control of genotype and sequence data; meta-analysis; gene x gene interaction; sample size estimation and evaluating power for common and rare variants. Programs that will be taught and utilized by course participants include: ANNOVAR, BEAM3, CADD, GERP, GotCloud, GenAbel, PLINK, Polyphen-2, R, SEQPower, Variant Association Tools (VAT), etc. Since gene mapping is a quickly changing field, the topics and analytic programs will be updated and changed annually to reflect the latest developments in the field of statistical genetics. Given the large increases in the amount of genetic data being generated, and in particular sequence data, it is extremely important to train researchers and give them the necessary information and tools for data analysis to elucidate the etiology of complex traits.